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ibdreg (version 0.2.5)

Regression Methods for IBD Linkage With Covariates

Description

A method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.

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Version

Install

install.packages('ibdreg')

Monthly Downloads

103

Version

0.2.5

License

GPL-2 | file LICENSE

Maintainer

Jason Sinnwell

Last Published

April 20th, 2013

Functions in ibdreg (0.2.5)

plot.linkage.all

Plot a linkage.all object

Linkage test statistics for ALL relative pairs

print.linkage.tests

Print a linkage.tests object

Compute mixture proportions, w, for mixture chi-square distribution

Print a nice banner

Regression Methods to Test for Linkage With Covariates

plot.ibdreg.unexpect

Plot unconstrained and constrained linkage tests to indicate areas of unexpected allele sharing

Linkage tests for relative pair groups

Create an ibd.var object via simulations using gene-dropping

calculate moments (mean, variance) for simulated ibd vectors

plot.linkage.tests

Plot a linkage.tests object

Merge ibd and covariate data

find the rows of a data frame with the minimum pvalue

set-up functions for sim.mark.prop

plot an ibdreg object

track system resources

lsConstrain.fit

Minimize Inequality Constrained Mahalanobis Distance

Combine person-specific covariates to pair-specific

Plot the -log10 of pvalues

print.linkage.all

Print or summarize a linkage.all object

create an ibd.var object

align ibd.var object with relative pairs within pairs.frame object

Compute Generalized Inverse of Input Matrix

cumulative probability of a chibar distribution

print an ibd.var object

Create an ibd.dat object

Create and return a data.frame with ibd data from merlin

Simulate Marker Propagation

create.pairs.frame

create a data frame for relative pairs

print and ibdreg object